cdtmc/mdc-labels · Datasets at Hugging Face

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aries and unenriched libraries from 17 samples using Illumina platforms. Mitochondrial genome reconstruction and analysis We prepared raw sequence data for alignment and mapped the filtered reads to the horse reference mitochondrial genome (Genbank: NC_001640.1) a	0
re available at the ENCODE portal (www.encodeproject.org) under the following accessions: ENCSR480YCS, ENCSR451UAK, ENCSR502KJC, ENCSR981LWT, ENCSR593JKE, ENCSR376OQT, ENCSR970YPW, ENCSR282MAC, ENCSR551OAQ, ENCSR529CSY, ENCSR117DKP, ENCSR117AJU, and ENCSR935NWB. ChI	0
ARG00000020057 Bone morphogenetic protein receptor, type II b (BMPR2B) 0.089 309,269 ENSDARG00000028533 Microtubule-actin crosslinking factor 1a (MACF1A) 0.193 18,761 ENSDARG00000037079 Cilia and flagella associated protein 36 (CFAP36) 0.136 154,823 ENSDARG00000043963 si:c	0
ii, Myotis lucifugus and Myotis davidii (Vespertilionidae). All new sequences were deposited into GeneBank with accession numbers KT345715-KT345725. Nrf2 sequences from five other mammal species were obtained from the Ensembl Database: Homo sapiens (ENSG00000116044), Pa	0
008 169.6 245 226.4 29.2 129 65 C:98%[S:77%,D:21%],F:1% 43,986 C:99%[S:72%,D:26%],F:1% GCA_904047255.1 As_ASTE806 Adineta steineri 160.3 7,597 168.2 257 222.5 29.2 145 82 C:96%[S:72%,D:24%],F:2% 45,930 C:98%[S:74%,D:24%],F:2% GCA_904047275.1 Dc_	0
/C 47.8 DRD2 rs1076562 11 113,296,008 G/A 42.1 DRD2 rs2734842 11 113,280,274 G/C 46.7 DRD2/ANKK1 rs2734849 11 113,270,160 T/C 24.5 DRD3 rs11721264 3 113,879,404 G/A 41.4 DRD3 rs167770 3 113,879,562 A/G 42.2 DRD3 rs3773678 3 113,870,078 C/T 32.0 DRD3 rs963468 3 11	0
1/BD2 This paper, https://www.sasbdb.org SASDCU2 ChIP-seq data of BRD3 WT and BRD3 BD(1:2)mut This paper, https://www.ebi.ac.uk/ arrayexpress E-MTAB-5670 ChIP-seq data in U2-OS for H3K27ac, H3K4me3, and H3K4me1 https://www.ncbi.nlm.nih.gov/geo/ GEO: GSE44672 ChIP	0
cotyle rugosa (T) Pseudoplatystoma reticulatum MHNG-PLAT-22374 AJ238835 Zehnder et al. 1999 13.9-14.7 Postgangesia inarmata Silurus glanis MHNG-PLAT-34212 AM931032 de Chambrier et al. 2008 12.5 Proteocephalidae gen. sp. Amia calva *MHNG-PLAT-35548 FM956088 de C	0
equence identity Sequence coverage Sequence range GMQE AlphaFold plDDt AlphaFold ipTM+pTM NheA 4k1p.1.A NheA 97.22% 0.93 42386 0.88 93.86 - NheB 7nmq.1.A Hbl-L1 40.82% 0.85 52397 0.69 83.42 - NheC 7nmq.1.A Hbl-L1 36.83% 0.88 44358 0.68 90.25 - Hbl-B 2nrj.1.A	0
mbospondin 2; RefSeq_ID: NM_003247.2), G REM1 (gremlin 1; RefSeq_ID: NM_013372.5), MMP11 (matrix-metalloproteinase 11; RefSeq_ID: NM_00594 0.3), COL11A1 (collagen type XI-alpha 1; RefSeq_ID: NM_001854.2), COL10A1 (collagen type X-alpha 1; RefSeq_ID: NM_000493.3), CS	0
L1111 LEP1GSC087 PRJNA74089 Bulgarica Mallika LEP1GSC007 PRJNA65041 Canicola Fiocruz LV133 LEP1GSC069 PRJNA167235 Copenhageni Fiocruz L1-130 LIC PRJNA10687 Lai 56601 LA PRJNA293 Lai IPAV LIF PRJNA32553 Linhai 56609 LIL PRJNA217894 Hardjo Norma G436 PRJNA185511 Mani	0
re transport system permease protein DKPENOPO_00656 DKPENOPO_04830 DKPENOPO_04831 yfiY COG0614 putative siderophore-binding lipoprotein YfiY DKPENOPO_04916 phoD COG3540 Alkaline phosphatase D Solubilization of organic phosphate DKPENOPO_01284 phoA COG1785 Alka	0
ipsychotic drugs. Additive genetic model was tested and the analysis was carried out in the total group and in subgroup stratified by the use of risperidone/paliperidone. Results: One statistically significant association between polymorphic variant rs1799836 of M	0
ion SRP023548. Samples in this dataset have a wide range of RIN values: three samples with RIN value of 10 (SRR873838, SRR873834 and SRR873822), two samples with RIN value of 8 (SRR879615 and SRR879800), three samples with RIN value of 6 (SRR880232, SRR881272 and	0
e break- down of dopamine in the brain [34]. MAO-B is widely Table 3 List of analyzed polymorphic variants of the dopamine transporter gene and the monoamine oxidase genes Gene SNP Chromosome Chromosome position Alleles Minor Allele Frequency SLC6A3 rs3756450 5 1,	0
hot Functional Cluster (enrichment score) Category Term and Description Genes P-Value Fold Enrichment Cluster 1 (3.24) INTERPRO IPR014760:Serum albumin, N-terminal ENSOARG00000013782 (ALB), ENSOARG00000012835 (GC), ENSOARG00000013966 (AFP), ENSOARG00000014129 (AFM	0
stasis and identifying critical regulatory genes are important for the treatment of this disease. This study aimed to identify differentially expressed genes (gene signature) and pathways that contribute to oral cancer metastasis to lymph nodes. The GSE70604-asso	0
h the following accession numbers; E-GEOD- 19722, E-GEOD-28654, E-GEOD-29623, E-GEOD- 39084, E-GEOD-45216, E-GEOD-45670, E-GEOD- 46474, E-GEOD-48278, E-GEOD-48350, E-GEOD- 48780, E-GEOD-49243, E-GEOD-50774, E-GEOD- 53224, E-GEOD-53890, E-GEOD-54543, E-GEOD- 54837, E-	0
cellia coryphicephala (T) Salminus brasiliensis MHNG-PLAT-17984 AJ238832 Zehnder et al. 1999 18.5 Nomimoscolex admonticellia Pinirampus pirinampu MHNG-PLAT-21870 AJ388628 Zehnder et al. 1999 7.1 Nomimoscolex chubbi Gymnotus carapo *MHNG-PLAT-20351 AJ388625 Zehn	0
20C 98.6% Saliva 4 01.28.2021 EPI_ISL_2340662 B.1 GH 20A 98.9% Saliva 5 01.05.2021 EPI_ISL_2340614 B.1.1 GR 20B 99.1% Saliva 6 01.05.2021 EPI_ISL_2340615 B.1.1 GR 20B 99% Saliva 7 01.13.2021 EPI_ISL_2340626 B.1.1.519 GR 20B 99.2% Saliva 8 04.01.2021 EPI_ISL_2340570 B.1.	0
obtained from the genomics data repository Gene Expression Omnibus (GEO). Microarray transcriptome datasets of FACS- purified microglia from 8.5 mo old WT (n = 5), TREM2 /(n = 4), 5xFAD (n = 5) and TREM2 //5xFAD (n = 6) mice were obtained from GEO (GSE65067). GE	0
oci have lost one branch of the ancient duplication (i.e. tetraploidy is degenerate). To 999 check that the putative RdRP expansion was indeed eukaryotic in origin, rather than viral, the 1000 HMMs for four viral RdRP families (PF00680, PF00978, PF00998 and	0
[9] Nomenclature CD52 CD80 CD86 cytotoxic T-lymphocyte- associated protein 4 (CD152) programmed cell death 1 (CD279) CD300a Common abbreviation CTLA-4 PD-1 HGNC, UniProt CD52, P31358 CD80, P33681 CD86, P42081 CTLA4, P16410 PDCD1, Q15116 CD300A, Q9UGN4 Endo	0
sitive E. albertii LB 5% TSB Pond water with 10% pigeon droppings RM9973 American crow (Corvus brachyrhynchos)/2009 SAMN12620691 + + RM9974 American crow (Corvus brachyrhynchos)/2009 SAMN12620692 RM9976 American crow (Corvus brachyrhynchos)/2009 SAMN12620693 + +	0
40 [36] E-GEOD-48278 57 [37] E-GEOD-48350 83 [38, 39] E-GEOD-48780 49 [40] E-GEOD-49243 73 [41, 42] E-GEOD-50774 21 [43] E-GEOD-53224 53 [44] E-GEOD-53890 41 [45] E-GEOD-54543 30 [46] E-GEOD-54837 226 [47] E-GEOD-58697 124 [48] E-GEOD-59312 79 [49] E-GEOD-60028 24 [	0
ssemblies for A. steineri, R. sordida and R. sp. Silwood-1 are indicated with diamond 226 and circle symbols, respectively. The four previously published genomes for A. vaga (Av2013, GenBank 227 accession GCA_000513175.1) and A. ricciae (Ar2018, GCA_900240375.1), R.	0
d in the 3 region, several G-rich motifs were found that are capable of assembling into G4 structures. A model of the RJF TNF gene was obtained by aligning 18 reads (Additional file 6) extracted from the two PacBio datasets described above using the MF000729.1 se	0
he percent of PacBio reads we could match to the ribosomal and SV2A gene sequences using blastn and blasr, to the expected value based on the existing genome assembly and PacBio read genome coverage. For the ribosomal gene sequence (accession number KT445834, 11,	0
turb-Seq (7d), Perturb-Seq (13d), and CRIS- PRi) separately by using the R package scran (version 1.11.27) [42]. Human Cell Atlas study This scRNA-seq dataset originates from a benchmark study of the Human Cell Atlas project and is available on GEO (GSE133549) [22	0
during the current study available from the corresponding author on reasonable request. The sequences of the genes used in this study are available at Genbank (https://www.ncbi.nlm.nih. gov/genbank/), and the accession numbers are as follows: PsCHS, JN105300.1; PsC	0
ose and subcutaneous adipose tissues (Fig. 4b). These results confirmed that the efficiency of cDNA synthesis widely depends on the replication ability the RT. Following these findings, we searched PacBio RNA-seq projects (PRJEB13246, PRJEB13248 and PRJEB12891 [46]	0
says. Batch adjustment method improves prediction performance in biological test sets with batch effects PLOS ONE \| https://doi.org/10.1371/journal.pone.0212669 February 22, 2019 2 / 15 60028, E-GEOD-61804, E-GEOD-63626, E-GEOD- 64415, E-GEOD-64857, E-GEOD-67851, E-G	0
scripts are available and version controlled at https://github.com/weng-lab/BENGI [35]. cCREs are available at the ENCODE portal (www.encodeproject.org) under the following accessions: ENCSR480YCS, ENCSR451UAK, ENCSR502KJC, ENCSR981LWT, ENCSR593JKE, ENCSR376OQT, ENC	0
CDL) user on 01 April 2025 Data availability All RNA-sequencing and Bisulfite-Sequencing data are available at the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (Edgar et al. 2002) through GEO Series acces- sion number GSE132167. Fig	0
BLVRA 0 5 0 5 HPA042865 0 1.08 18 73 0 Q08629 Testican-1 (protein SPOCK) SPOCK1 112 0 0 0 HPA007450 0 1.58 0 100 0 Q12907 Lectin mannose-binding 2 LMAN2 2 9 2 0 HPA003927 0 1.64 0 82 0 Q96AG4 Leucine-rich repeat- containing protein 59 LRRC59 1 4 0 0 HPA030827 0 1.	0
017 H5N8 EPI1104284 2017 99% A/duck/Egypt/F446/2017 H5N8 EPI1018208 2017-04-07 99% A/Eur_Wig/NL-Greonterp/16015653-001/2016 H5N8 EPI1019551 2016-12-08 99% A/swan/Italy/17VIR537-2/2017 H5N8 EPI954552 2017-01-19 99% NA A/chicken/Egypt/D10700/2015 H9N2 KX000734* 201	0
isassembly. Nomenclature tubulin alpha 1a tubulin alpha 4a tubulin beta class I tubulin beta 3 class III tubulin beta 4B class IVb tubulin beta 8 class VIII HGNC, UniProt TUBA1A, Q71U36 TUBA4A, P68366 TUBB, P07437 TUBB3, Q13509 TUBB4B, P68371 TUBB8, Q3ZCM7 Inhi	0
,270,160 T/C 24.5 DRD3 rs11721264 3 113,879,404 G/A 41.4 DRD3 rs167770 3 113,879,562 A/G 42.2 DRD3 rs3773678 3 113,870,078 C/T 32.0 DRD3 rs963468 3 113,862,887 G/A 27.2 DRD3 rs7633291 3 113,887,068 T/G 22.4 DRD3 rs2134655 3 113,858,201 G/A 20.3 DRD3 rs9817063 3 11	0
6, 68, 88, 104], with demcizumab and tarextumab iden- tified as antibody inhibitors of ligand:receptor binding [74]. Nomenclature notch receptor 1 notch receptor 2 notch receptor 3 notch receptor 4 HGNC, UniProt NOTCH1, P46531 NOTCH2, Q04721 NOTCH3, Q9UM47 NOTC	0
ng the specific primer pair of 515F (5- GTGCCAGCMGCCGCGGTAA-3) and 806R (5 -GGACTACHV GGGTWTCTAAT-3), targeting the V3V4 hypervariable region. The data that supporting this study are openly available in the NCBI GenBank (BioProject accession number: PRJNA664798). St	0
atty acids and cholesterol [58]. Nomenclature retinol binding protein 1 retinol binding protein 2 retinol binding protein 3 retinol binding protein 4 retinol binding protein 5 retinol binding protein 7 HGNC, UniProt RBP1, P09455 RBP2, P50120 RBP3, P10745 RBP4	0
rmedia Ictalurus punctatus MHNG-PLAT-25795 AJ275232 de Chambrier et al. 2004c 11.3 Crepidobothrium gerrardii (T) Boa constrictor MHNG-PLAT-66546 KC786018 Scholz et al. 2013 3.6 Electrotaenia malopteruri (T) Malapterurus electricus *MHNG-PLAT-33995 JX477434 Ash	0
er candidates for breast cancer Accession no. Protein name Gene name MS MS spectral count HPA database MCF-7 MDA- MB-231 SK- BR-3 Hs578T HPA Ab Average IHC score Percent of location Normal Breast cancer n c m c m n Q99538 Legumain LGMN 7 24 13 1 HPA001426 1 2	0
305T (GCA_000165715.3), Rubinisphaera italica Pan54T (GCA_007859715.1), Rubinisphaera margarita ICM_H10T (GCA_022267515.1), Schlesneria paludi- cola MPL7T (GCA_000255655.1), Symmachiella dynata Mal52T (GCA_007747995.1), Symmachiella dynata Pan258 (GCA_007744975.1), Sy	0
ts are rather unexpected. Since the grass carp has been cultured for Table 4 Annotation of candidate genes under putative selection consistently identified by both outlier tests and Bayenv association tests Locus Annotation Gene name Overall Fst 428 ENSDARG00000010097 Coag	0
erland), the extent of the genome coverage was more than 80. Assessment of the quality of genome assembly was performed using the program Quast 5.0 [36], the genomic sequence of B. anthracis Ames Ancestor strain (GeneBank: NC_007530.2, NC_ 007322.2, NC_007323.3) was	0
both replicates from GEO (GSM3630200, GSM3630201), which include Holland et al. Genome Biology (2020) 21:36 Page 16 of 19 sgRNA counts next to the rest of the transcription. We refrained from using the targeted sequencing of the sgRNA in GSM3630202, GSM	0
acid sequences for the VH and VL regions for these bispecific antibodies are summarized in online supplemental table 3. Each BsAb was produced using the Expi293 expression system (Thermo Fisher Scientific RRID:CVCL_D615) or HEK 293 T cell (RRID:CVCL_KS61) and	0
950644 This study A. laevigata 18729 14684 3881 22 2 13 KC346251 Rodovalho et al., 2014 A. opaciceps 19257 14840 4433 22 2 13 KY9[50643 This study A. texana 19709 14844 4880 22 2 13 MF417380 This study A. sexdens rubropilosa 19748 14513 5235 22 2 13 MF591717 This	0
.59 35.31 GCA_000021785.1 Periodontitis ATCC10876 5.94 34.80 GCA_000160895.1 Nd F837/76 5.29 35.40 GCA_000239195.1 Enteritis Rock4-2 5.77 34.90 GCA_000161275.1 Soil Q1 5.51 35.50 GCA_000013065.1 Nd BGSC6E1 5.73 35.00 GCA_000160915.1 Nd CI 5.49 35.27 GCA_000143605.1 Anth	0
BD1/BD2 This paper, https://www.sasbdb.org SASDCR2 Small-angle scattering data and models of tandem BRDT BD1/BD2 This paper, https://www.sasbdb.org SASDCU2 ChIP-seq data of BRD3 WT and BRD3 BD(1:2)mut This paper, https://www.ebi.ac.uk/ arrayexpress E-MTAB-5670 ChIP	0
olled at https://github.com/weng-lab/BENGI [35]. cCREs are available at the ENCODE portal (www.encodeproject.org) under the following accessions: ENCSR480YCS, ENCSR451UAK, ENCSR502KJC, ENCSR981LWT, ENCSR593JKE, ENCSR376OQT, ENCSR970YPW, ENCSR282MAC, ENCSR551OAQ, ENC	0
tgangesia inarmata Silurus glanis MHNG-PLAT-34212 AM931032 de Chambrier et al. 2008 12.5 Proteocephalidae gen. sp. Amia calva MHNG-PLAT-35548 FM956088 de Chambrier et al. 2009a 9.3 Proteocephalus filicollis Gasterosteus aculeatus *MHNG-PLAT-24081 AJ388636 Zehn	0
t one branch of the ancient duplication (i.e. tetraploidy is degenerate). To 999 check that the putative RdRP expansion was indeed eukaryotic in origin, rather than viral, the 1000 HMMs for four viral RdRP families (PF00680, PF00978, PF00998 and PF02123) wer	0
982 proteomes from a selection of eukaryotic species to represent the diversity and distribution of 983 Argonaute, Dicer and RdRP proteins were downloaded (June 2020) from UniProt and subjected 984 to the same procedure: Arabidopsis thaliana (UP000006548), Or	0
of isolation GenBank BioSample Number aSwimming Motility stx2f -positive E. albertii LB 5% TSB Pond water with 10% pigeon droppings RM9973 American crow (Corvus brachyrhynchos)/2009 SAMN12620691 + + RM9974 American crow (Corvus brachyrhynchos)/2009 SAMN12620692 R	0
an . Species Host species Voucher number Accession Number Reference Surface ovary % Acanthotaenia shipleyi (T) Varanus salvator MHNG-PLAT-32887 AJ583453 de Chambrier et al. 2004c 6.8 Ageneiella brevifilis (T) Ageneiosus inermis *MHNG-PLAT-21841 AJ388600 Zehn	0
l. 1999 5.0 Ophiotaenia saphena Lithobates pipiens MHNG-PLAT-32851 KP729402 This paper 8.3-8.7 Pangasiocestus romani (T) Pangasius larnaudii MHNG-PLAT-75449 KP729397 This paper 10.6 Paraproteocephalus parasiluri (T) Silurus asotus *MHNG-PLAT-22438 AJ388604 Zehn	0
a high output mode run 101 bp paired-end reads using an Illumina HiSeq 2500 at the Hubbard Center for Genome Studies at the University of New Hampshire. The Illumina reads were aligned to the published reference ES114 strain (PRJNA58163, assem- bly GCA_000011805.1) usi	0
SAMN12620702 RM15115 White-Breasted Nuthatch (Sitta carolinensis)/2011 SAMN12620703 RM15116 Oregon Junco (Junco hyemalis)/2011 SAMN12620704 2011C-4180 Human/2011 SAMN03019926 2012EL-1823B Human/2012 SAMN04498560 2014C-4015 Human/2014 SAMN04505646 2	0
rg/10.5281/zenodo.4311473. The qRT-PCR data from the initial screen was deposited along with processed data from follow-up experiments to BioStudies database at EMBL-EBI (Sarkans et al., 2018; https://www.ebi.ac.uk/biostudies) under accession number S-BSST447. RNA	0
nce per species (Supplementary Appendix S6 available on Dryad). To allow the position of the root to be inferred, corresponding genes or regions from Megachile sculpturalis (GenBank accession NC_028017) and/or Megachile strupigera (GenBank accession KT346366) wer	0
93 + + RM10507 Brown-headed cowbird (Molothrus ater)/2009 SAMN12620694 + + + RM10705 Brown-headed cowbird (Molothrus ater)/2009 SAMN12620697 + + + RM15112 Oregon Junco (Junco hyemalis)/2011 SAMN12620700 RM15113 Oregon Junco (Junco hyemalis)/2011 SAMN12620701 R	0
unco hyemalis)/2011 SAMN12620701 RM15114 Oregon Junco (Junco hyemalis)/2011 SAMN12620702 RM15115 White-Breasted Nuthatch (Sitta carolinensis)/2011 SAMN12620703 RM15116 Oregon Junco (Junco hyemalis)/2011 SAMN12620704 2011C-4180 Human/2011 SAMN03019926 2	0
1126 GC GC, vitamin D binding protein [Source:HGNC Symbol;Acc:HGNC:4187] ENSOARG00000012835 6 86619919 86657661 ENSBTAG00000013718 6 88695940 88739180 AFP alpha fetoprotein [Source:HGNC Symbol;Acc:HGNC:317] ENSOARG00000013966 6 88166794 88190190 ENSBTAG00000017131 6 90	0
c epitopes in trans, and thus contributing to the assembly of large BET complexes on chromatin. (D) Crystal structure of BRD4/BD1 bound to an E2F1 di-Kac peptide (K117ac-XX-K120ac motif) or the previously published histone H4 K5ac/K8ac peptide (PDB: 3UVW). (E	0
in microglia. We also referenced this dataset to serve as a background of all identifiable proteins in mouse brain. Purified microglial transcriptomics CD11b+ microglia microarray datasets from wild-type and 5xFAD mice were obtained from GEO dataset GSE65067 [24]	0
roli Enr17T (GCA_007754425.1), Gimesia maris CA11 (GCA_007747015.1), Gimesia panareensis Pan110T (GCA_007748015.1), Maioricimonas rariso- cia Mal4T (GCA_007747795.1), Planctomicrobium piriforme P3T (GCA_900113665.1), Planctopirus ephydatiae spb1T (GCA_007752345.1), Pl	0
calculations were performed in the R statistical en- vironment using basic R functions and the SNPassoc package [43]. Results From the list of 38 SNPs studied of dopamine receptor genes and SLC6A3 genes we excluded 4 SNPs (rs6275, rs6347, rs2550956, rs11133767) wit	0
nical proteins) mapped Solid samples Mucosa, colorectal adenoma, colorectal carcinoma Colorectum PXD001676 [58] E-PROT-103 16 No 16 8 9,711 215,033 196,017 8,949 PXD002137 [59] E-PROT-104 192 Yes (6) 32 25 PXD014511 [60] E-PROT-105 310 Yes (5) 62 52 PXD019504 [61]	0
Transcription factor regulators NF-B regulators S19 Tubulins Tumour-associated antigens WD repeat-containing proteins Adiponectin receptors Other protein targets Adiponectin receptors Overview: Adiponectin receptors (provisional nomen- clature, ENSFM00500000270960)	0
10T (GCA_022267515.1), Schlesneria paludi- cola MPL7T (GCA_000255655.1), Symmachiella dynata Mal52T (GCA_007747995.1), Symmachiella dynata Pan258 (GCA_007744975.1), Symmachiella macrocystis CA54T (GCA_007860075.1), Thalassoglobus neptunius KOR42T (GCA_007859735.1), Th	0
.gz from https://gtexportal.org/home/datasets. crisprQTL data is available from the supplemental tables in Gasperini et al. [20]. ENCODE RNA-seq experiments are available at the ENCODE portal under the following accessions: ENCSR000COQ, ENCSR000CPR, ENCSR000AEM, ENC	0
ction of eukaryotic species to represent the diversity and distribution of 983 Argonaute, Dicer and RdRP proteins were downloaded (June 2020) from UniProt and subjected 984 to the same procedure: Arabidopsis thaliana (UP000006548), Oryza sativa (UP000007015), 9	0
22,216 39.7 1,141 61 32 433 63 C:98%[S:81%,D:17%],F:1% 40,289 C:99%[S:74%,D:26%],F:0% GCA_903995855.1 Rg_MAG3 Rotaria magnacalcarata 180.9 22,132 40.7 1,142 60 32 508 60 C:96%[S:80%,D:17%],F:1% 40,740 C:99%[S:77%,D:22%],F:0% GCA_903995845.1 Rg_	0
mons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: The sequenced genome was submitted to GenBank under BioProject PRJNA296687 with	0
is located on microchro- mosome 25 [37]. Using these two sequences as queries we searched the two RJF PacBio projects (accession numbers SRR2028042-SRR2028057 and SRR2028138- SRR2028233, 190 Gb., ~180X genome coverage, PacBio RS 2.3.0.0.140640) and SRR5444488-SRR5	0
below included analyses of 10 available complete genomes of Wolbachia and 4 draft genomes (Table S8): wMel, Wolbachia from Drosophila melanogaster (NC_002978), wCau, Wolbachia from Carposina sasakii (CP041215) and wNfla, Wolbachia from Nomada flava (LYUW00000000) for	0
search article Genomics and Evolutionary Biology Appendix 2table 2 continued Partitions Outgroup Hippidion? Included Excluded Topology 1 2 3 6 1/2/3 4/6 5/7 All Tapirus terrestris (AJ428947) 0.456 0.317 0.205 0.018 0.549 0.313 0.139 Tapirus indicus (NC023838) 0.2	0
1 IPR029787 Nucleotide cyclase GO:0007165 Signal transduction ORTHO03S004748 0.75 0.02 IPR036452 Ribonucleoside hydrolase GO:0016614 Digestive enzyme ORTHO03S005894 0.75 0.01 IPR008139 Saposin B type domain Digestive enzyme ORTHO03S004453 0.72 0.05 IPR017920 COMM	0
s and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License Nomenclature Adipo1 receptor Adipo2 receptor HGNC, UniProt ADIPOR1, Q96A54 ADIP	0
/2016 H5N8 EPI1019551 2016-12-08 99% A/swan/Italy/17VIR537-2/2017 H5N8 EPI954552 2017-01-19 99% NA A/chicken/Egypt/D10700/2015 H9N2 KX000734* 2015-02-26 97% A/chicken/Egypt/S107569A/2015 H9N2 KX000727* 2015-02-15 97% A/chicken/Egypt/A1093D/2015 H9N2 KX000717* 201	0
il Q1 5.51 35.50 GCA_000013065.1 Nd BGSC6E1 5.73 35.00 GCA_000160915.1 Nd CI 5.49 35.27 GCA_000143605.1 Anthrax F65185 6.13 34.70 GCA_000161315.1 Wound E33L 5.84 35.17 GCA_000833045.1 Carcass Rock3-28 6.04 35.75 GCA_000161195.1 Soil AH187 5.60 35.52 GCA_000021225.1 Nd R	0
sequences analyzed in this study are as follows: GSE95356 (H3K4me2/me3) and GSE73406 (RNA) for S. cerevisiae [11]; GSE49733 (H3K4me2), GSE49739 (H3K4me3), and GSE100723 (RNA) for C. elegans (http://www.modencode.org); GSE98967 (H3K4me2/me3) and GSE98966 (RNA	0
on microchro- mosome 25 [37]. Using these two sequences as queries we searched the two RJF PacBio projects (accession numbers SRR2028042-SRR2028057 and SRR2028138- SRR2028233, 190 Gb., ~180X genome coverage, PacBio RS 2.3.0.0.140640) and SRR5444488-SRR5444513 (63	0
of PCR products, as specified in Supplemental Information Table S1. Methods for obtain ing the new sequences from PCR/Sanger sequencing are given in Maddison (2012). New sequences have been submitted to GenBank with accession numbers MK838494 to MK838511. We	0
75 0.221323 > 0.999 O14980 XPO1_HUMAN XPO1 Exportin-1 1.804 0.000086 0.0026 P55060 XPO2_HUMAN CSE1L Exportin-2 1.530 0.011327 0.1659 Q9HAV4 XPO5_HUMAN XPO5 Exportin-5 1.698 0.000021 0.0008 P12270 TPR_HUMAN TPR Nucleoprotein TPR 1.121 0.001823 0.0330 Q9UKX7 NUP5	0
o LPS-treated wild-type microglia as well as comparing wild-type vs. 5xFAD microglia. Human post-mortem brain proteomics data Protein expression data were obtained from ProteomeX- change (http://proteomecentral.proteomexchange.org/ cgi/GetDataset?ID=PXD007160) [14	0
on for hereditary breast cancer in Taiwan (N = 480) (Continued) Gene HGVS notation Type of variant No. of carriers SNP ID RAD50 NM_005732.3:c.2157dupA (p.Glu723Glyfs) Frameshift 1 rs397507178 RAD51C NM_058216.2:c.394dupA (p.Thr132Asnfs) Frameshift 1 rs730881940 RAD5	0
of mRNA sequencing of untreated vs. I-CBP112 treated organoids, 4 biol replicates per group. Selected genes are highlighted. (E) mRNA sequencing of untreated vs. I-CBP112 treated organoids. GSEA of LGR5+ stem cell signature from Muoz et al. (2012) (GSE33949). No	0
mbrier et al. 2004c 6.2-10.2 Nupelia portoriquensis (T) Sorubim lima MHNG-PLAT-34185 KP729401 This paper 10.3 Ophiotaenia bungari Bungarus fasciatus MHNG-PLAT-75442 KC786022 Scholz et al. 2013 3.1 Ophiotaenia europaea Natrix maura *MHNG-PLAT-18407 AJ388598 Zehn	0
noma, colorectal carcinoma Colorectum PXD001676 [58] E-PROT-103 16 No 16 8 9,711 215,033 196,017 8,949 PXD002137 [59] E-PROT-104 192 Yes (6) 32 25 PXD014511 [60] E-PROT-105 310 Yes (5) 62 52 PXD019504 [61] E-PROT-106 74 No 74 37 CPTAC PDC000111 [31] E-PROT-23 1425	0
uture 425 study as we seek to understand the forces shaping sex chromosomes. 426 Materials and methods 427 Alignment and variant-calling 428 Whole-genome sequencing reads were obtained from the European Nucleotide Archive (PRJEB9450, PRJEB11742, 429 PRJEB14673, PRJ	0
iella piracatinga Calophysus macropterus MHNG-PLAT-19868 AJ388627 Zehnder et al. 1999 10.4 Rudolphiella szidati Luciopimelodus pati MHNG-PLAT-24668 AJ388617 de Chambrier et al. 2004c 14.4 Sandonella sandoni (T) Heterotis niloticus *MHNG-PLAT-49356 AM931033 Unpu	0
liva 5 01.05.2021 EPI_ISL_2340614 B.1.1 GR 20B 99.1% Saliva 6 01.05.2021 EPI_ISL_2340615 B.1.1 GR 20B 99% Saliva 7 01.13.2021 EPI_ISL_2340626 B.1.1.519 GR 20B 99.2% Saliva 8 04.01.2021 EPI_ISL_2340570 B.1.1.7 GRY 20I (Alpha) 100% Saliva 9 04.06.2021 EPI_ISL_2340575 B.1.	0
3,862,887 G/A 27.2 DRD3 rs7633291 3 113,887,068 T/G 22.4 DRD3 rs2134655 3 113,858,201 G/A 20.3 DRD3 rs9817063 3 113,847,108 C/T 42.8 DRD3 rs324035 3 113,868,854 C/A 40.2 DRD3 rs1800828 3 113,891,549 G/C 22.2 DRD3 rs167771 3 113,876,275 A/G 41.1 DRD3 rs6280 3 11	0
e Name Clinical Stage According CHEMBL Chemical Formula Plate A, D2 Antifungals MMV1634386 CHEMBL3311228 https://www.ebi.ac.uk/chembl/compound_ report_card/CHEMBL3311228/ Oteseconazole 3 (Phase III) C23 H16 F7 N5 O2 Plate A, E2 Antifungals MMV637528 CHEMBL64391 http	0
ing and processed RNASeq data from this study have been deposited into the NCBI GEO database under accession number GSE71651 (http://www.ncbi.nlm. nih.gov/geo/query/acc.cgi?token=obcxosaur xoppwx & acc = GSE71651). Access and analysis of public data GDS723, GDS	0
mal bronchial epithelium cells collected during bronchoscopy from non-smokers, former smok- ers, and current smokers. Samples are selected from various studies, which are divided into three batches A (GSE994 [24], GSE4115 [25, 26], GSE7895 [27]), B (GSE66499, [28	0
3.0 software (Roche, Switzerland), the extent of the genome coverage was more than 80. Assessment of the quality of genome assembly was performed using the program Quast 5.0 [36], the genomic sequence of B. anthracis Ames Ancestor strain (GeneBank: NC_007530.2, NC_	0

aries and unenriched libraries from 17 samples using Illumina platforms. Mitochondrial genome reconstruction and analysis We prepared raw sequence data for alignment and mapped the filtered reads to the horse reference mitochondrial genome (Genbank: NC_001640.1) a

0

re available at the ENCODE portal (www.encodeproject.org) under the following accessions: ENCSR480YCS, ENCSR451UAK, ENCSR502KJC, ENCSR981LWT, ENCSR593JKE, ENCSR376OQT, ENCSR970YPW, ENCSR282MAC, ENCSR551OAQ, ENCSR529CSY, ENCSR117DKP, ENCSR117AJU, and ENCSR935NWB. ChI

0

ARG00000020057 Bone morphogenetic protein receptor, type II b (BMPR2B) 0.089 309,269 ENSDARG00000028533 Microtubule-actin crosslinking factor 1a (MACF1A) 0.193 18,761 ENSDARG00000037079 Cilia and flagella associated protein 36 (CFAP36) 0.136 154,823 ENSDARG00000043963 si:c

0

ii, Myotis lucifugus and Myotis davidii (Vespertilionidae). All new sequences were deposited into GeneBank with accession numbers KT345715-KT345725. Nrf2 sequences from five other mammal species were obtained from the Ensembl Database: Homo sapiens (ENSG00000116044), Pa

0

008 169.6 245 226.4 29.2 129 65 C:98%[S:77%,D:21%],F:1% 43,986 C:99%[S:72%,D:26%],F:1% GCA_904047255.1 As_ASTE806 Adineta steineri 160.3 7,597 168.2 257 222.5 29.2 145 82 C:96%[S:72%,D:24%],F:2% 45,930 C:98%[S:74%,D:24%],F:2% GCA_904047275.1 Dc_

0

/C 47.8 DRD2 rs1076562 11 113,296,008 G/A 42.1 DRD2 rs2734842 11 113,280,274 G/C 46.7 DRD2/ANKK1 rs2734849 11 113,270,160 T/C 24.5 DRD3 rs11721264 3 113,879,404 G/A 41.4 DRD3 rs167770 3 113,879,562 A/G 42.2 DRD3 rs3773678 3 113,870,078 C/T 32.0 DRD3 rs963468 3 11

0

1/BD2 This paper, https://www.sasbdb.org SASDCU2 ChIP-seq data of BRD3 WT and BRD3 BD(1:2)mut This paper, https://www.ebi.ac.uk/ arrayexpress E-MTAB-5670 ChIP-seq data in U2-OS for H3K27ac, H3K4me3, and H3K4me1 https://www.ncbi.nlm.nih.gov/geo/ GEO: GSE44672 ChIP

0

cotyle rugosa (T) Pseudoplatystoma reticulatum *MHNG-PLAT-22374 AJ238835 Zehnder et al. 1999 13.9-14.7 Postgangesia inarmata Silurus glanis *MHNG-PLAT-34212 AM931032 de Chambrier et al. 2008 12.5 Proteocephalidae gen. sp. Amia calva *MHNG-PLAT-35548 FM956088 de C

0

equence identity Sequence coverage Sequence range GMQE AlphaFold plDDt AlphaFold ipTM+pTM NheA 4k1p.1.A NheA 97.22% 0.93 42386 0.88 93.86 - NheB 7nmq.1.A Hbl-L1 40.82% 0.85 52397 0.69 83.42 - NheC 7nmq.1.A Hbl-L1 36.83% 0.88 44358 0.68 90.25 - Hbl-B 2nrj.1.A

0

mbospondin 2; RefSeq_ID: NM_003247.2), G REM1 (gremlin 1; RefSeq_ID: NM_013372.5), MMP11 (matrix-metalloproteinase 11; RefSeq_ID: NM_00594 0.3), COL11A1 (collagen type XI-alpha 1; RefSeq_ID: NM_001854.2), COL10A1 (collagen type X-alpha 1; RefSeq_ID: NM_000493.3), CS

0

L1111 LEP1GSC087 PRJNA74089 Bulgarica Mallika LEP1GSC007 PRJNA65041 Canicola Fiocruz LV133 LEP1GSC069 PRJNA167235 Copenhageni Fiocruz L1-130 LIC PRJNA10687 Lai 56601 LA PRJNA293 Lai IPAV LIF PRJNA32553 Linhai 56609 LIL PRJNA217894 Hardjo Norma G436 PRJNA185511 Mani

0

re transport system permease protein DKPENOPO_00656 DKPENOPO_04830 DKPENOPO_04831 yfiY COG0614 putative siderophore-binding lipoprotein YfiY DKPENOPO_04916 phoD COG3540 Alkaline phosphatase D Solubilization of organic phosphate DKPENOPO_01284 phoA COG1785 Alka

0

ipsychotic drugs. Additive genetic model was tested and the analysis was carried out in the total group and in subgroup stratified by the use of risperidone/paliperidone. Results: One statistically significant association between polymorphic variant rs1799836 of M

0

ion SRP023548. Samples in this dataset have a wide range of RIN values: three samples with RIN value of 10 (SRR873838, SRR873834 and SRR873822), two samples with RIN value of 8 (SRR879615 and SRR879800), three samples with RIN value of 6 (SRR880232, SRR881272 and

0

e break- down of dopamine in the brain [34]. MAO-B is widely Table 3 List of analyzed polymorphic variants of the dopamine transporter gene and the monoamine oxidase genes Gene SNP Chromosome Chromosome position Alleles Minor Allele Frequency SLC6A3 rs3756450 5 1,

0

hot Functional Cluster (enrichment score) Category Term and Description Genes P-Value Fold Enrichment Cluster 1 (3.24) INTERPRO IPR014760:Serum albumin, N-terminal ENSOARG00000013782 (ALB), ENSOARG00000012835 (GC), ENSOARG00000013966 (AFP), ENSOARG00000014129 (AFM

0

stasis and identifying critical regulatory genes are important for the treatment of this disease. This study aimed to identify differentially expressed genes (gene signature) and pathways that contribute to oral cancer metastasis to lymph nodes. The GSE70604-asso

0

h the following accession numbers; E-GEOD- 19722, E-GEOD-28654, E-GEOD-29623, E-GEOD- 39084, E-GEOD-45216, E-GEOD-45670, E-GEOD- 46474, E-GEOD-48278, E-GEOD-48350, E-GEOD- 48780, E-GEOD-49243, E-GEOD-50774, E-GEOD- 53224, E-GEOD-53890, E-GEOD-54543, E-GEOD- 54837, E-

0

cellia coryphicephala (T) Salminus brasiliensis *MHNG-PLAT-17984 AJ238832 Zehnder et al. 1999 18.5 Nomimoscolex admonticellia Pinirampus pirinampu *MHNG-PLAT-21870 AJ388628 Zehnder et al. 1999 7.1 Nomimoscolex chubbi Gymnotus carapo *MHNG-PLAT-20351 AJ388625 Zehn

0

20C 98.6% Saliva 4 01.28.2021 EPI_ISL_2340662 B.1 GH 20A 98.9% Saliva 5 01.05.2021 EPI_ISL_2340614 B.1.1 GR 20B 99.1% Saliva 6 01.05.2021 EPI_ISL_2340615 B.1.1 GR 20B 99% Saliva 7 01.13.2021 EPI_ISL_2340626 B.1.1.519 GR 20B 99.2% Saliva 8 04.01.2021 EPI_ISL_2340570 B.1.

0

obtained from the genomics data repository Gene Expression Omnibus (GEO). Microarray transcriptome datasets of FACS- purified microglia from 8.5 mo old WT (n = 5), TREM2 /(n = 4), 5xFAD (n = 5) and TREM2 //5xFAD (n = 6) mice were obtained from GEO (GSE65067). GE

0

oci have lost one branch of the ancient duplication (i.e. tetraploidy is degenerate). To 999 check that the putative RdRP expansion was indeed eukaryotic in origin, rather than viral, the 1000 HMMs for four viral RdRP families (PF00680, PF00978, PF00998 and

0

[9] Nomenclature CD52 CD80 CD86 cytotoxic T-lymphocyte- associated protein 4 (CD152) programmed cell death 1 (CD279) CD300a Common abbreviation CTLA-4 PD-1 HGNC, UniProt CD52, P31358 CD80, P33681 CD86, P42081 CTLA4, P16410 PDCD1, Q15116 CD300A, Q9UGN4 Endo

0

sitive E. albertii LB 5% TSB Pond water with 10% pigeon droppings RM9973 American crow (Corvus brachyrhynchos)/2009 SAMN12620691 + + RM9974 American crow (Corvus brachyrhynchos)/2009 SAMN12620692 RM9976 American crow (Corvus brachyrhynchos)/2009 SAMN12620693 + +

0

40 [36] E-GEOD-48278 57 [37] E-GEOD-48350 83 [38, 39] E-GEOD-48780 49 [40] E-GEOD-49243 73 [41, 42] E-GEOD-50774 21 [43] E-GEOD-53224 53 [44] E-GEOD-53890 41 [45] E-GEOD-54543 30 [46] E-GEOD-54837 226 [47] E-GEOD-58697 124 [48] E-GEOD-59312 79 [49] E-GEOD-60028 24 [

0

ssemblies for A. steineri, R. sordida and R. sp. Silwood-1 are indicated with diamond 226 and circle symbols, respectively. The four previously published genomes for A. vaga (Av2013, GenBank 227 accession GCA_000513175.1) and A. ricciae (Ar2018, GCA_900240375.1), R.

0

d in the 3 region, several G-rich motifs were found that are capable of assembling into G4 structures. A model of the RJF TNF gene was obtained by aligning 18 reads (Additional file 6) extracted from the two PacBio datasets described above using the MF000729.1 se

0

he percent of PacBio reads we could match to the ribosomal and SV2A gene sequences using blastn and blasr, to the expected value based on the existing genome assembly and PacBio read genome coverage. For the ribosomal gene sequence (accession number KT445834, 11,

0

turb-Seq (7d), Perturb-Seq (13d), and CRIS- PRi) separately by using the R package scran (version 1.11.27) [42]. Human Cell Atlas study This scRNA-seq dataset originates from a benchmark study of the Human Cell Atlas project and is available on GEO (GSE133549) [22

0

during the current study available from the corresponding author on reasonable request. The sequences of the genes used in this study are available at Genbank (https://www.ncbi.nlm.nih. gov/genbank/), and the accession numbers are as follows: PsCHS, JN105300.1; PsC

0

ose and subcutaneous adipose tissues (Fig. 4b). These results confirmed that the efficiency of cDNA synthesis widely depends on the replication ability the RT. Following these findings, we searched PacBio RNA-seq projects (PRJEB13246, PRJEB13248 and PRJEB12891 [46]

0

says. Batch adjustment method improves prediction performance in biological test sets with batch effects PLOS ONE | https://doi.org/10.1371/journal.pone.0212669 February 22, 2019 2 / 15 60028, E-GEOD-61804, E-GEOD-63626, E-GEOD- 64415, E-GEOD-64857, E-GEOD-67851, E-G

0

scripts are available and version controlled at https://github.com/weng-lab/BENGI [35]. cCREs are available at the ENCODE portal (www.encodeproject.org) under the following accessions: ENCSR480YCS, ENCSR451UAK, ENCSR502KJC, ENCSR981LWT, ENCSR593JKE, ENCSR376OQT, ENC

0

CDL) user on 01 April 2025 Data availability All RNA-sequencing and Bisulfite-Sequencing data are available at the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (Edgar et al. 2002) through GEO Series acces- sion number GSE132167. Fig

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BLVRA 0 5 0 5 HPA042865 0 1.08 18 73 0 Q08629 Testican-1 (protein SPOCK) SPOCK1 112 0 0 0 HPA007450 0 1.58 0 100 0 Q12907 Lectin mannose-binding 2 LMAN2 2 9 2 0 HPA003927 0 1.64 0 82 0 Q96AG4 Leucine-rich repeat- containing protein 59 LRRC59 1 4 0 0 HPA030827 0 1.

0

017 H5N8 EPI1104284 2017 99% A/duck/Egypt/F446/2017 H5N8 EPI1018208 2017-04-07 99% A/Eur_Wig/NL-Greonterp/16015653-001/2016 H5N8 EPI1019551 2016-12-08 99% A/swan/Italy/17VIR537-2/2017 H5N8 EPI954552 2017-01-19 99% NA A/chicken/Egypt/D10700/2015 H9N2 KX000734* 201

0

isassembly. Nomenclature tubulin alpha 1a tubulin alpha 4a tubulin beta class I tubulin beta 3 class III tubulin beta 4B class IVb tubulin beta 8 class VIII HGNC, UniProt TUBA1A, Q71U36 TUBA4A, P68366 TUBB, P07437 TUBB3, Q13509 TUBB4B, P68371 TUBB8, Q3ZCM7 Inhi

0

,270,160 T/C 24.5 DRD3 rs11721264 3 113,879,404 G/A 41.4 DRD3 rs167770 3 113,879,562 A/G 42.2 DRD3 rs3773678 3 113,870,078 C/T 32.0 DRD3 rs963468 3 113,862,887 G/A 27.2 DRD3 rs7633291 3 113,887,068 T/G 22.4 DRD3 rs2134655 3 113,858,201 G/A 20.3 DRD3 rs9817063 3 11

0

6, 68, 88, 104], with demcizumab and tarextumab iden- tified as antibody inhibitors of ligand:receptor binding [74]. Nomenclature notch receptor 1 notch receptor 2 notch receptor 3 notch receptor 4 HGNC, UniProt NOTCH1, P46531 NOTCH2, Q04721 NOTCH3, Q9UM47 NOTC

0

ng the specific primer pair of 515F (5- GTGCCAGCMGCCGCGGTAA-3) and 806R (5 -GGACTACHV GGGTWTCTAAT-3), targeting the V3V4 hypervariable region. The data that supporting this study are openly available in the NCBI GenBank (BioProject accession number: PRJNA664798). St

0

atty acids and cholesterol [58]. Nomenclature retinol binding protein 1 retinol binding protein 2 retinol binding protein 3 retinol binding protein 4 retinol binding protein 5 retinol binding protein 7 HGNC, UniProt RBP1, P09455 RBP2, P50120 RBP3, P10745 RBP4

0

rmedia Ictalurus punctatus *MHNG-PLAT-25795 AJ275232 de Chambrier et al. 2004c 11.3 Crepidobothrium gerrardii (T) Boa constrictor *MHNG-PLAT-66546 KC786018 Scholz et al. 2013 3.6 Electrotaenia malopteruri (T) Malapterurus electricus *MHNG-PLAT-33995 JX477434 Ash

0

er candidates for breast cancer Accession no. Protein name Gene name MS MS spectral count HPA database MCF-7 MDA- MB-231 SK- BR-3 Hs578T HPA Ab Average IHC score Percent of location Normal Breast cancer n c m c m n Q99538 Legumain LGMN 7 24 13 1 HPA001426 1 2

0

305T (GCA_000165715.3), Rubinisphaera italica Pan54T (GCA_007859715.1), Rubinisphaera margarita ICM_H10T (GCA_022267515.1), Schlesneria paludi- cola MPL7T (GCA_000255655.1), Symmachiella dynata Mal52T (GCA_007747995.1), Symmachiella dynata Pan258 (GCA_007744975.1), Sy

0

ts are rather unexpected. Since the grass carp has been cultured for Table 4 Annotation of candidate genes under putative selection consistently identified by both outlier tests and Bayenv association tests Locus Annotation Gene name Overall Fst 428 ENSDARG00000010097 Coag

0

erland), the extent of the genome coverage was more than 80. Assessment of the quality of genome assembly was performed using the program Quast 5.0 [36], the genomic sequence of B. anthracis Ames Ancestor strain (GeneBank: NC_007530.2, NC_ 007322.2, NC_007323.3) was

0

both replicates from GEO (GSM3630200, GSM3630201), which include Holland et al. Genome Biology (2020) 21:36 Page 16 of 19 sgRNA counts next to the rest of the transcription. We refrained from using the targeted sequencing of the sgRNA in GSM3630202, GSM

0

acid sequences for the VH and VL regions for these bispecific antibodies are summarized in online supplemental table 3. Each BsAb was produced using the Expi293 expression system (Thermo Fisher Scientific RRID:CVCL_D615) or HEK 293 T cell (RRID:CVCL_KS61) and

0

950644 This study A. laevigata 18729 14684 3881 22 2 13 KC346251 Rodovalho et al., 2014 A. opaciceps 19257 14840 4433 22 2 13 KY9[50643 This study A. texana 19709 14844 4880 22 2 13 MF417380 This study A. sexdens rubropilosa 19748 14513 5235 22 2 13 MF591717 This

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.59 35.31 GCA_000021785.1 Periodontitis ATCC10876 5.94 34.80 GCA_000160895.1 Nd F837/76 5.29 35.40 GCA_000239195.1 Enteritis Rock4-2 5.77 34.90 GCA_000161275.1 Soil Q1 5.51 35.50 GCA_000013065.1 Nd BGSC6E1 5.73 35.00 GCA_000160915.1 Nd CI 5.49 35.27 GCA_000143605.1 Anth

0

BD1/BD2 This paper, https://www.sasbdb.org SASDCR2 Small-angle scattering data and models of tandem BRDT BD1/BD2 This paper, https://www.sasbdb.org SASDCU2 ChIP-seq data of BRD3 WT and BRD3 BD(1:2)mut This paper, https://www.ebi.ac.uk/ arrayexpress E-MTAB-5670 ChIP

0

olled at https://github.com/weng-lab/BENGI [35]. cCREs are available at the ENCODE portal (www.encodeproject.org) under the following accessions: ENCSR480YCS, ENCSR451UAK, ENCSR502KJC, ENCSR981LWT, ENCSR593JKE, ENCSR376OQT, ENCSR970YPW, ENCSR282MAC, ENCSR551OAQ, ENC

0

tgangesia inarmata Silurus glanis *MHNG-PLAT-34212 AM931032 de Chambrier et al. 2008 12.5 Proteocephalidae gen. sp. Amia calva *MHNG-PLAT-35548 FM956088 de Chambrier et al. 2009a 9.3 Proteocephalus filicollis Gasterosteus aculeatus *MHNG-PLAT-24081 AJ388636 Zehn

0

t one branch of the ancient duplication (i.e. tetraploidy is degenerate). To 999 check that the putative RdRP expansion was indeed eukaryotic in origin, rather than viral, the 1000 HMMs for four viral RdRP families (PF00680, PF00978, PF00998 and PF02123) wer

0

982 proteomes from a selection of eukaryotic species to represent the diversity and distribution of 983 Argonaute, Dicer and RdRP proteins were downloaded (June 2020) from UniProt and subjected 984 to the same procedure: Arabidopsis thaliana (UP000006548), Or

0

of isolation GenBank BioSample Number aSwimming Motility stx2f -positive E. albertii LB 5% TSB Pond water with 10% pigeon droppings RM9973 American crow (Corvus brachyrhynchos)/2009 SAMN12620691 + + RM9974 American crow (Corvus brachyrhynchos)/2009 SAMN12620692 R

0

an *. Species Host species Voucher number Accession Number Reference Surface ovary % Acanthotaenia shipleyi (T) Varanus salvator *MHNG-PLAT-32887 AJ583453 de Chambrier et al. 2004c 6.8 Ageneiella brevifilis (T) Ageneiosus inermis *MHNG-PLAT-21841 AJ388600 Zehn

0

l. 1999 5.0 Ophiotaenia saphena Lithobates pipiens *MHNG-PLAT-32851 KP729402 This paper 8.3-8.7 Pangasiocestus romani (T) Pangasius larnaudii *MHNG-PLAT-75449 KP729397 This paper 10.6 Paraproteocephalus parasiluri (T) Silurus asotus *MHNG-PLAT-22438 AJ388604 Zehn

0

a high output mode run 101 bp paired-end reads using an Illumina HiSeq 2500 at the Hubbard Center for Genome Studies at the University of New Hampshire. The Illumina reads were aligned to the published reference ES114 strain (PRJNA58163, assem- bly GCA_000011805.1) usi

0

SAMN12620702 RM15115 White-Breasted Nuthatch (Sitta carolinensis)/2011 SAMN12620703 RM15116 Oregon Junco (Junco hyemalis)/2011 SAMN12620704 2011C-4180 Human/2011 SAMN03019926 2012EL-1823B Human/2012 SAMN04498560 2014C-4015 Human/2014 SAMN04505646 2

0

rg/10.5281/zenodo.4311473. The qRT-PCR data from the initial screen was deposited along with processed data from follow-up experiments to BioStudies database at EMBL-EBI (Sarkans et al., 2018; https://www.ebi.ac.uk/biostudies) under accession number S-BSST447. RNA

0

nce per species (Supplementary Appendix S6 available on Dryad). To allow the position of the root to be inferred, corresponding genes or regions from Megachile sculpturalis (GenBank accession NC_028017) and/or Megachile strupigera (GenBank accession KT346366) wer

0

93 + + RM10507 Brown-headed cowbird (Molothrus ater)/2009 SAMN12620694 + + + RM10705 Brown-headed cowbird (Molothrus ater)/2009 SAMN12620697 + + + RM15112 Oregon Junco (Junco hyemalis)/2011 SAMN12620700 RM15113 Oregon Junco (Junco hyemalis)/2011 SAMN12620701 R

0

unco hyemalis)/2011 SAMN12620701 RM15114 Oregon Junco (Junco hyemalis)/2011 SAMN12620702 RM15115 White-Breasted Nuthatch (Sitta carolinensis)/2011 SAMN12620703 RM15116 Oregon Junco (Junco hyemalis)/2011 SAMN12620704 2011C-4180 Human/2011 SAMN03019926 2

0

1126 GC GC, vitamin D binding protein [Source:HGNC Symbol;Acc:HGNC:4187] ENSOARG00000012835 6 86619919 86657661 ENSBTAG00000013718 6 88695940 88739180 AFP alpha fetoprotein [Source:HGNC Symbol;Acc:HGNC:317] ENSOARG00000013966 6 88166794 88190190 ENSBTAG00000017131 6 90

0

c epitopes in trans, and thus contributing to the assembly of large BET complexes on chromatin. (D) Crystal structure of BRD4/BD1 bound to an E2F1 di-Kac peptide (K117ac-XX-K120ac motif) or the previously published histone H4 K5ac/K8ac peptide (PDB: 3UVW). (E

0

in microglia. We also referenced this dataset to serve as a background of all identifiable proteins in mouse brain. Purified microglial transcriptomics CD11b+ microglia microarray datasets from wild-type and 5xFAD mice were obtained from GEO dataset GSE65067 [24]

0

roli Enr17T (GCA_007754425.1), Gimesia maris CA11 (GCA_007747015.1), Gimesia panareensis Pan110T (GCA_007748015.1), Maioricimonas rariso- cia Mal4T (GCA_007747795.1), Planctomicrobium piriforme P3T (GCA_900113665.1), Planctopirus ephydatiae spb1T (GCA_007752345.1), Pl

0

calculations were performed in the R statistical en- vironment using basic R functions and the SNPassoc package [43]. Results From the list of 38 SNPs studied of dopamine receptor genes and SLC6A3 genes we excluded 4 SNPs (rs6275, rs6347, rs2550956, rs11133767) wit

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nical proteins) mapped Solid samples Mucosa, colorectal adenoma, colorectal carcinoma Colorectum PXD001676 [58] E-PROT-103 16 No 16 8 9,711 215,033 196,017 8,949 PXD002137 [59] E-PROT-104 192 Yes (6) 32 25 PXD014511 [60] E-PROT-105 310 Yes (5) 62 52 PXD019504 [61]

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Transcription factor regulators NF-B regulators S19 Tubulins Tumour-associated antigens WD repeat-containing proteins Adiponectin receptors Other protein targets Adiponectin receptors Overview: Adiponectin receptors (provisional nomen- clature, ENSFM00500000270960)

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10T (GCA_022267515.1), Schlesneria paludi- cola MPL7T (GCA_000255655.1), Symmachiella dynata Mal52T (GCA_007747995.1), Symmachiella dynata Pan258 (GCA_007744975.1), Symmachiella macrocystis CA54T (GCA_007860075.1), Thalassoglobus neptunius KOR42T (GCA_007859735.1), Th

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.gz from https://gtexportal.org/home/datasets. crisprQTL data is available from the supplemental tables in Gasperini et al. [20]. ENCODE RNA-seq experiments are available at the ENCODE portal under the following accessions: ENCSR000COQ, ENCSR000CPR, ENCSR000AEM, ENC

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ction of eukaryotic species to represent the diversity and distribution of 983 Argonaute, Dicer and RdRP proteins were downloaded (June 2020) from UniProt and subjected 984 to the same procedure: Arabidopsis thaliana (UP000006548), Oryza sativa (UP000007015), 9

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22,216 39.7 1,141 61 32 433 63 C:98%[S:81%,D:17%],F:1% 40,289 C:99%[S:74%,D:26%],F:0% GCA_903995855.1 Rg_MAG3 Rotaria magnacalcarata 180.9 22,132 40.7 1,142 60 32 508 60 C:96%[S:80%,D:17%],F:1% 40,740 C:99%[S:77%,D:22%],F:0% GCA_903995845.1 Rg_

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mons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: The sequenced genome was submitted to GenBank under BioProject PRJNA296687 with

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is located on microchro- mosome 25 [37]. Using these two sequences as queries we searched the two RJF PacBio projects (accession numbers SRR2028042-SRR2028057 and SRR2028138- SRR2028233, 190 Gb., ~180X genome coverage, PacBio RS 2.3.0.0.140640) and SRR5444488-SRR5

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below included analyses of 10 available complete genomes of Wolbachia and 4 draft genomes (Table S8): wMel, Wolbachia from Drosophila melanogaster (NC_002978), wCau, Wolbachia from Carposina sasakii (CP041215) and wNfla, Wolbachia from Nomada flava (LYUW00000000) for

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search article Genomics and Evolutionary Biology Appendix 2table 2 continued Partitions Outgroup Hippidion? Included Excluded Topology 1 2 3 6 1/2/3 4/6 5/7 All Tapirus terrestris (AJ428947) 0.456 0.317 0.205 0.018 0.549 0.313 0.139 Tapirus indicus (NC023838) 0.2

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1 IPR029787 Nucleotide cyclase GO:0007165 Signal transduction ORTHO03S004748 0.75 0.02 IPR036452 Ribonucleoside hydrolase GO:0016614 Digestive enzyme ORTHO03S005894 0.75 0.01 IPR008139 Saposin B type domain Digestive enzyme ORTHO03S004453 0.72 0.05 IPR017920 COMM

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s and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License Nomenclature Adipo1 receptor Adipo2 receptor HGNC, UniProt ADIPOR1, Q96A54 ADIP

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/2016 H5N8 EPI1019551 2016-12-08 99% A/swan/Italy/17VIR537-2/2017 H5N8 EPI954552 2017-01-19 99% NA A/chicken/Egypt/D10700/2015 H9N2 KX000734* 2015-02-26 97% A/chicken/Egypt/S107569A/2015 H9N2 KX000727* 2015-02-15 97% A/chicken/Egypt/A1093D/2015 H9N2 KX000717* 201

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il Q1 5.51 35.50 GCA_000013065.1 Nd BGSC6E1 5.73 35.00 GCA_000160915.1 Nd CI 5.49 35.27 GCA_000143605.1 Anthrax F65185 6.13 34.70 GCA_000161315.1 Wound E33L 5.84 35.17 GCA_000833045.1 Carcass Rock3-28 6.04 35.75 GCA_000161195.1 Soil AH187 5.60 35.52 GCA_000021225.1 Nd R

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sequences analyzed in this study are as follows: GSE95356 (H3K4me2/me3) and GSE73406 (RNA) for S. cerevisiae [11]; GSE49733 (H3K4me2), GSE49739 (H3K4me3), and GSE100723 (RNA) for C. elegans (http://www.modencode.org); GSE98967 (H3K4me2/me3) and GSE98966 (RNA

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on microchro- mosome 25 [37]. Using these two sequences as queries we searched the two RJF PacBio projects (accession numbers SRR2028042-SRR2028057 and SRR2028138- SRR2028233, 190 Gb., ~180X genome coverage, PacBio RS 2.3.0.0.140640) and SRR5444488-SRR5444513 (63

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of PCR products, as specified in Supplemental Information Table S1. Methods for obtain ing the new sequences from PCR/Sanger sequencing are given in Maddison (2012). New sequences have been submitted to GenBank with accession numbers MK838494 to MK838511. We

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75 0.221323 > 0.999 O14980 XPO1_HUMAN XPO1 Exportin-1 1.804 0.000086 0.0026 P55060 XPO2_HUMAN CSE1L Exportin-2 1.530 0.011327 0.1659 Q9HAV4 XPO5_HUMAN XPO5 Exportin-5 1.698 0.000021 0.0008 P12270 TPR_HUMAN TPR Nucleoprotein TPR 1.121 0.001823 0.0330 Q9UKX7 NUP5

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o LPS-treated wild-type microglia as well as comparing wild-type vs. 5xFAD microglia. Human post-mortem brain proteomics data Protein expression data were obtained from ProteomeX- change (http://proteomecentral.proteomexchange.org/ cgi/GetDataset?ID=PXD007160) [14

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on for hereditary breast cancer in Taiwan (N = 480) (Continued) Gene HGVS notation Type of variant No. of carriers SNP ID RAD50 NM_005732.3:c.2157dupA (p.Glu723Glyfs) Frameshift 1 rs397507178 RAD51C NM_058216.2:c.394dupA (p.Thr132Asnfs) Frameshift 1 rs730881940 RAD5

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of mRNA sequencing of untreated vs. I-CBP112 treated organoids, 4 biol replicates per group. Selected genes are highlighted. (E) mRNA sequencing of untreated vs. I-CBP112 treated organoids. GSEA of LGR5+ stem cell signature from Muoz et al. (2012) (GSE33949). No

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mbrier et al. 2004c 6.2-10.2 Nupelia portoriquensis (T) Sorubim lima *MHNG-PLAT-34185 KP729401 This paper 10.3 Ophiotaenia bungari Bungarus fasciatus *MHNG-PLAT-75442 KC786022 Scholz et al. 2013 3.1 Ophiotaenia europaea Natrix maura *MHNG-PLAT-18407 AJ388598 Zehn

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noma, colorectal carcinoma Colorectum PXD001676 [58] E-PROT-103 16 No 16 8 9,711 215,033 196,017 8,949 PXD002137 [59] E-PROT-104 192 Yes (6) 32 25 PXD014511 [60] E-PROT-105 310 Yes (5) 62 52 PXD019504 [61] E-PROT-106 74 No 74 37 CPTAC PDC000111 [31] E-PROT-23 1425

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uture 425 study as we seek to understand the forces shaping sex chromosomes. 426 Materials and methods 427 Alignment and variant-calling 428 Whole-genome sequencing reads were obtained from the European Nucleotide Archive (PRJEB9450, PRJEB11742, 429 PRJEB14673, PRJ

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iella piracatinga Calophysus macropterus *MHNG-PLAT-19868 AJ388627 Zehnder et al. 1999 10.4 Rudolphiella szidati Luciopimelodus pati *MHNG-PLAT-24668 AJ388617 de Chambrier et al. 2004c 14.4 Sandonella sandoni (T) Heterotis niloticus *MHNG-PLAT-49356 AM931033 Unpu

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liva 5 01.05.2021 EPI_ISL_2340614 B.1.1 GR 20B 99.1% Saliva 6 01.05.2021 EPI_ISL_2340615 B.1.1 GR 20B 99% Saliva 7 01.13.2021 EPI_ISL_2340626 B.1.1.519 GR 20B 99.2% Saliva 8 04.01.2021 EPI_ISL_2340570 B.1.1.7 GRY 20I (Alpha) 100% Saliva 9 04.06.2021 EPI_ISL_2340575 B.1.

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3,862,887 G/A 27.2 DRD3 rs7633291 3 113,887,068 T/G 22.4 DRD3 rs2134655 3 113,858,201 G/A 20.3 DRD3 rs9817063 3 113,847,108 C/T 42.8 DRD3 rs324035 3 113,868,854 C/A 40.2 DRD3 rs1800828 3 113,891,549 G/C 22.2 DRD3 rs167771 3 113,876,275 A/G 41.1 DRD3 rs6280 3 11

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e Name Clinical Stage According CHEMBL Chemical Formula Plate A, D2 Antifungals MMV1634386 CHEMBL3311228 https://www.ebi.ac.uk/chembl/compound_ report_card/CHEMBL3311228/ Oteseconazole 3 (Phase III) C23 H16 F7 N5 O2 Plate A, E2 Antifungals MMV637528 CHEMBL64391 http

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ing and processed RNASeq data from this study have been deposited into the NCBI GEO database under accession number GSE71651 (http://www.ncbi.nlm. nih.gov/geo/query/acc.cgi?token=obcxosaur xoppwx & acc = GSE71651). Access and analysis of public data GDS723, GDS

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mal bronchial epithelium cells collected during bronchoscopy from non-smokers, former smok- ers, and current smokers. Samples are selected from various studies, which are divided into three batches A (GSE994 [24], GSE4115 [25, 26], GSE7895 [27]), B (GSE66499, [28

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3.0 software (Roche, Switzerland), the extent of the genome coverage was more than 80. Assessment of the quality of genome assembly was performed using the program Quast 5.0 [36], the genomic sequence of B. anthracis Ames Ancestor strain (GeneBank: NC_007530.2, NC_

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